Otto Heinrich Warburg was born in Freiburg im Breisgau in 1883, close to the Swiss border. Otto's mother was the daughter of a Protestant family of Bankers and civil servants from Baden. His father, Emil Warburg, had converted to Protestantism as an adult, although Emil’s parents were Orthodox Jews. Emil was a member of the illustrious Warburg family of Altona, and had converted to Christianity reportedly after a disagreement with his Conservative Jewish parents. Emil was also President of the Physikalische Reichsanstalt, Wirklicher Geheimer Oberregierungsrat (True Senior Privy Counselor).

Otto Warburg studied chemistry under the famous Emil Fischer, and earned his Doctor of chemistry in Berlin in 1906. He then studied under Ludolf von Krehl and earned the degree of Doctor of Medicine in Heidelberg in 1911.

Between 1908 and 1914, Warburg was affiliated with the Naples Marine Biological Station, (in Naples), Italy, where he conducted research. In later years, he would return for visits, and maintained a lifelong friendship with the family of the station's Director, Anton Dohrn.

In 1918, Warburg was appointed professor at the Kaiser Wilhelm Institute for Biology in Berlin-Dahlem (part of the Kaiser-Wilhelm-Gesellschaft). By 1931 he was named Director of the Kaiser Wilhelm Institute for Cell Physiology, which was founded the previous year by a donation of the Rockefeller Foundation to the Kaiser Wilhelm Gesellschaft (since renamed the Max Planck Society).

Otto Warburg edited and had much of his original work published in The Metabolism of Tumours (tr. 1931) and wrote New Methods of Cell Physiology (1962). An unabashed anglophile, Otto Warburg was thrilled when Oxford University awarded him an honorary doctorate. He was awarded the Order Pour le Mérite in 1952 and was known to tell other universities not to bother with honorary doctorates. He would ask officials to mail him medals he had been awarded so as to avoid a ceremony that would separate him from his beloved laboratory.

Nobel Laureate George Wald, having completed his Ph.D. in zoology at Columbia University, received an award from the U.S. National Research Council to study with Warburg. During his time with Warburg, 1932-1933, Wald discovered vitamin A in the retina.

According to the Reichsbürgergesetz from 1935 (cf. Nuremberg Laws) Warburg was considered by the Nazis a half-Jew (Halbjude) resp. Mischling and in September 1942 he issued an official request for equal status ("Gleichstellung") with Germans, which was granted.

In 1941, Warburg lost his post briefly when he made critical remarks about the regime, but a few weeks later a personal order from Hitler's Chancellery ordered him to resume work on his cancer research. Göring also arranged for him to be Classified as one-quarter Jewish.

In 1943 Warburg relocated his laboratory to the village of Liebenburg on the outskirts of Berlin to avoid ongoing air attacks.

In 1944, Warburg was nominated for a second Nobel Prize in Physiology by Albert Szent-Györgyi, for his work on nicotinamide, the mechanism and enzymes involved in fermentation, and the discovery of flavin (in yellow enzymes). Some sources report that he was selected to receive the award that year, but was prevented from receiving it by Adolf Hitler’s regime, which had issued a decree in 1937 that forbade Germans from accepting Nobel Prizes. According to the Nobel Foundation, this rumor is not true; although he was considered a worthwhile candidate, he was not selected for the prize at that time.

The Otto Warburg Medal is intended to commemorate Warburg's outstanding achievements. It has been awarded by the German Society for Biochemistry and Molecular Biology (Gesellschaft für Biochemie und Molekularbiologie) since 1963. The prize honors and encourages pioneering achievements in fundamental biochemical and molecular biological research. The Otto Warburg Medal is regarded as the highest award in Germany for biochemists and molecular biologists. It has been endowed with prize money, sponsored by the publishing company Elsevier/BBA.

In 1968, he suffered a broken femur. This was complicated by deep vein thrombosis. He died in 1970 from pulmonary embolism and was buried in a Christian cemetery.

However, a recent reevaluation of the data from nuclear/cytoplasm transfer experiments, where nuclei from cancer cells are placed in normal cytoplasm and where nuclei from normal cells are placed in cancer cytoplasm, more strongly supports Warburg’s original theory than the somatic mutation theory for the origin of malignant transformation and cancer.